theiagen/public_health_viral_genomics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
WDLAGPL-3.0
Issues
- 1
Pangolin_Update change
#163 opened by sage-wright - 1
- 0
wf_ivar_consensus obscures min_freq option
#221 opened by michellescribner - 0
Capture Freyja docker
#133 opened by sage-wright - 1
Freyja Updates needed
#124 opened by kevinlibuit - 2
Mercury Prep variable type parsing
#142 opened by sage-wright - 0
TheiaCov output - Nextclade_lineage empty
#195 opened by kapsakcj - 0
- 1
Mercury_Prep_N_Batch: fixes
#206 opened by sage-wright - 0
Add mincov to Freyja_Plot
#208 opened by sage-wright - 0
Freyja Small Changes
#169 opened by michellescribner - 0
Pangolin_Update redundant output variable
#197 opened by sage-wright - 2
IRMA fails with too many reads
#200 opened by frankambrosio3 - 1
- 2
Adding Illumina version of HIV-GC workflow
#145 opened by frankambrosio3 - 0
Add SIERRA to HIVGC
#147 opened by frankambrosio3 - 0
- 0
Mercury_Prep_N_Batch
#173 opened by kevinlibuit - 1
Add organism track for flu characterization
#191 opened by kevinlibuit - 1
- 2
ensure WDL compatibility with Azure
#187 opened by vsmalladi - 0
Implement workflow logic to use "mpox" as the target organism for TheiaCoV MPXV analysis
#192 opened by frankambrosio3 - 2
VADR for WNV
#180 opened by kevinlibuit - 3
add support for West Nile Virus
#114 opened by kapsakcj - 1
link to the notion page in 2.2.0
#188 opened by neranjan007 - 0
- 1
Aviti compatibility
#178 opened by kevinlibuit - 2
fastq-scan fails on large FASTQs
#183 opened by kapsakcj - 0
Adding alternative reference schemes for C-HIV
#146 opened by frankambrosio3 - 1
VADR for MPXV
#179 opened by kevinlibuit - 0
- 0
TheiaCoV_Illumina_* if MPXV reference is not found, will use SC2 rather than error
#168 opened by michellescribner - 0
iVar amino acid data not outputted
#167 opened by michellescribner - 0
- 1
Capture of extended pango lineage
#152 opened by kevinlibuit - 1
Update to Nextclade v2
#155 opened by kevinlibuit - 2
Update ReadTheDocs
#143 opened by kevinlibuit - 0
- 0
Add pol region coverage stat to HIVGC
#150 opened by frankambrosio3 - 0
- 0
- 0
Adding TheiaCoV_FASTA and Augur workflows
#135 opened by kevinlibuit - 1
add task for pangolin v4
#121 opened by kapsakcj - 2
s_gene_percent_coverage float and percent_gene_coverage file for ClearLabs and ONT
#129 opened by kapsakcj - 0
Output NextClade Data Set Tag utilized
#122 opened by kevinlibuit - 0
trimmomatic outputs not being saved
#119 opened by kevinlibuit - 0
Adding sc2rf task to TheiaCoV workflows
#123 opened by kevinlibuit - 0
Whitespace in ClearLabs assembly headers
#115 opened by sage-wright - 0
SAM Refiner
#117 opened by frankambrosio3 - 0